Construction of the linkage map

The data we used consisted in 418 markers, genotyped from an F\(_2\) population with 287 individuals. Some of these data were used to construct a linkage map in a previous work1. The linkage map was constructed using the onemap R package version 2.1.32.

We found 14 linkage groups, shown below. You can hover over the marker’s position with your mouse cursor to see more information.

Comparison with previous work

Below, we compare the marker order obtained here (left) with that presented in a previous work (right) for the fourteen linkage groups.

With the functions try_seq and rf_graph_table from the package onemap we could see the markers that fit or did not fit the map so well. We tried positions for markers that yielded a LOD score no lower than -3 by the try_seq function. Also, we removed markers whose presence modified the map too much, by increasing the total size by more than 7 cM or affecting the positioning of other markers.

Linkage group 1

In our map, the markers AAT267, BA129, BA374 were not included in the first linkage group. Also, the position of the marker AAT333 was changed, yielding a shorter map.

Linkage group 2

In the second group, the markers AA420, BA172 and CC132 that were in the previous version were not included.

Linkage group 3

In the third group, the marker BA384 was not included and BD286 was placed between CA220 and CB156.

Linkage group 4

In the fourth linkage group, CA384 and BD239 were not included.

Linkage group 5

CB230 was included in the fifth linkage group and AA378, CC342 and AA118C were removed.

Linkage group 6

In the sixth linkage group, AA227, AA158, BD169 and CC126 were not included.

Linkage group 7

The marker CB162 was added to the seventh group, BD209, AA280 and BB103C were filtered and AA361 were placed between CB162 and CA258C.

Linkage group 8

In linkage group 8, the markers AAT211, BA314 and CC338C were removed.

Linkage group 9

In linkage group 9, we added BA400 and BB176. Also, CA196 was placed between CA115 and AAT222.

Linkage group 10

The markers CA96, CC392 and AA153C were added to linkage group 10. Also, the marker AAT283 was placed at the extremity of the map. In the previous map, AAT283 was between BD433 and CB309.

Linkage group 11

In linkage group 11, the order of the markers CC61-BC526C-BA449 was changed to BA449-BC526-CC61. Also, AAT356 was placed between BD100 and BB124.

Linkage group 12

In linkage group 12, the position of the marker CA378 changed.

Linkage group 13

CA315 was added to linkage group 13. Also, the ordering of the markers BB198-BC199-BA145 changed to BA145-BC199-BB198.

Linkage group 14

In linkage group 14, the order of the markers BC80-CC320-AP3 changed to CC320-BC80-AP3.

Transmission Rate Distortion

Results of the tests for TRD for each marker are presented below. The p-value has been corrected for multiple tests using the Bonferroni procedure.

Below, these results can also be observed in relation to the marker position in our map. We found a region with four contiguous markers favoring the presence of the M. guttatus allele in linkage group 1 and a region with 14 markers in linkage group 11. In linkage group 14, there is a region with seven contiguous markers favoring M. nasutus allele, but there are 5 other markers on the other end of the linkage group favoring M. guttatus allele. These findings are similar to those reported in the previous work.

Discussion

  1. Fishman, L., Kelly, A. J., Morgan, E., & Willis, J. H. (2001). A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics, 159(4), 1701-1716. doi: 10.1093/genetics/159.4.1701 (URL: https://doi.org/10.1093/genetics/159.4.1701).↩︎

  2. Margarido, G., de Souza, A., Garcia, A. (2007). OneMap: software for genetic mapping in outcrossing species. Hereditas. doi: 10.1111/j.2007.0018-0661.02000.x (URL: https://doi.org/10.1111/j.2007.0018-0661.02000.x).↩︎